In recent years, a highly interesting pattern has emerged: Computer scientists release new research findings on arXiv and just days later, developers release an open-source implementation on GitHub. This pattern is immensely powerful. One could call it collaborative open computer science (cocs). GitXiv is a space to share links to open computer science projects.

For this years conference of the International Brain Research Organization a short movie has been produced featuring the Research Department of Neuroscience at the Ruhr University. PAM makes also a short appearance in this video :).

The hippocampus is a subcortical brain region that likely emerged in the common ancestors of mammals and amphibians. Its internal structure is very well conserved within mammals but differs considerably between different taxa. Its functional role in spatial navigation, however, seems to be important in all lineages. The hippocampus is therefore a prime candidate to study the relationship between the structure and function of large-scale networks and to differentiate between generic and species-specific properties of a network. But how can computational neuroscience help to uncover the general principles of nervous system organization and its species-specific implementations? In this talk, I will outline different approaches to use computational models for comparative neuroscience.
One of them will be a recently developed modeling paradigm, called Parametric Anatomical Modeling (PAM). PAM facilitates the translation of large-scale anatomical 3d data into a formal description of neural networks with connection patterns and connection lengths derived from anatomical features of the biological network (Pyka and Cheng 2014). Using a 3d model of the rat hippocampus and entorhinal cortex, we reconstructed the information flow within the hippocampal loop, that is the timing and temporal order, in which spiking activity propagates through the network. The simulations provide first insights of how spatial relations between different brain areas affect functional and other structural properties of the network. Additionally, our simulations of information flow help to constrain the space of more abstract computational models of the hippocampus.

The CA1-projecting axons of CA3 pyramidal cells, called Schaffer collaterals, constitute one of the major information flow routes in hippocampal formation. Recent anatomical studies have revealed the non-random structural connectivity between CA3 and CA1, but little is known regarding the functional connectivity (i.e., how CA3 network activity is functionally transmitted downstream to the CA1 network). Using functional multi-neuron calcium imaging of rat hippocampal slices, we monitored the spatiotemporal patterns of spontaneous CA3 and CA1 burst activity under pharmacological GABAergic blockade. We found that spatially clustered CA3 activity patterns were transformed into layered CA1 activity sequences. Specifically, synchronized bursts initiated from multiple hot spots in CA3 ensembles, and CA1 neurons located deeper in the pyramidal cell layer were recruited during earlier phases of the burst events. The order of these sequential activations was maintained across the bursts, but the sequence velocity varied depending on the inter-burst intervals. Thus, CA3 axons innervate CA1 neurons in a highly topographical fashion.